Proposal for Storing Whole Slide Images for Pathology in DICOM

1. Proposal for StoringWhole Slide Images for Pathology in DICOM DICOM Working Group 26 1/17/07

2. Agenda • Introduction • Description of Problem • Characteristics of Whole Slide Images • DICOM Limitations and Characteristics • Description of Proposed Solution

3. Introduction • Pathology is undergoing a transformation • Digital imaging is increasingly important • Driven by availability of instruments for digitizing microscope slides, resulting in whole-slide images (WSI) • WSI are different to other images stored in DICOM • Size - larger • Access patterns – pan, zoom, focus • It is desirable to support WSI for Pathology in DICOM • Will facilitate interoperability with other modalities • Will foster adoption of Digital Pathology

4. Description of ProblemCharacteristics of WSI Image dimensions, data size • Typical: 20mm x 15mm @ .25mpp (“40X”) = 80,000 x 60,000 pixels = 4.8Gp = 15GB • Extreme: 50mm x 25mm @ .1mpp (“100X”) =500,000 x 250,000 pixels = 125Gp = 375GB • x 10 Z-planes => 3.75TB

5. Description of ProblemCharacteristics of WSI Access patterns • Pathologists cannot view entire microscope slide at diagnostic resolution • Pan around at low res (2.5mpp = “4X”), then zoom in at high res (.25mpp = “40X”) • Requires organization to support rapid panning & zooming • Multiple Z-planes may be captured • Requires organization to support rapid focusing

6. image strips image pixels region (strips) to be loaded region to be viewed or processed Description of ProblemCharacteristics of WSI Simple image organization: Stripped Does not support efficient panning

7. image pixels image tiles region (tiles) to be loaded region to be viewed or processed Description of ProblemCharacteristics of WSI More complex image organization: Tiled Does support efficient panning

8. lower resolution, larger image region highest resolution, small image region Description of ProblemCharacteristics of WSI Still have an issue with zooming

9. Thumbnail Image (low resolution) Intermediate Zoom Image Tile Intermediate Zoom Image (intermediate resolution) Retrieved image region Baseline Image (highest resolution) Baseline Image Tile Description of ProblemCharacteristics of WSI Pyramid addresses zooming

10. Description of ProblemDICOM Limitations and Characteristics DICOM Limitations • 16-bit signed integer for pixel dimensions: 32K x 32K • 32-bit signed integer for image object size: 2GB • No subregion access to images

11. Description of ProblemDICOM Limitations and Characteristics DICOM Characteristics • Successful, widely adopted • An important reason why is extension process • DICOM extensions • Conservative – only extend standard when necessary, leverage existing standard • Encourage innovation – involve vendors in process, enable vendors to innovate within [extended] standard • Better products for market • Discourage proprietary solutions • Backward compatible – maximize compatibility with existing [non-extended] systems, degrade gracefully

12. Thumbnail Image Intermediate Image Tiles Baseline Image Tiles DICOM Series Description of Proposed SolutionStore WSI Pyramid as DICOM Series Each “tile” of each level of each plane of WSI corresponds to image in series

13. Description of Proposed SolutionStore WSI Pyramid as DICOM Series • Tile size can vary (240 … 1K … 4K … 32K) • Each resolution level stored separately in the series (typically thumbnail is first) • Each Z-plane stored separately in the series • Each image in series identified by coordinates • X, Y offsets • Zoom (resolution) • Z offset (plane)

14. Description of Proposed SolutionCharacteristics of Proposed Solution • Works around DICOM limitations • 16-bit pixel dimension: okay, tiles will be less than 32K x 32K • 32-bit image size: okay, tiles will be smaller than 2GB • No subregion access: okay, each tile is individually addressible as an image • Encompasses storage of single image in a series by itself as proper subset

15. Description of Proposed SolutionCharacteristics of Proposed Solution • Will require little change by PACS vendors • They already handle images in series • Degrades gracefully for existing DICOM viewers • Thumbnails / low-level images display “as is” • High-res images display as pieces of entire image • (Pathologists will require purpose built viewer) • Rapid pan, zoom, etc. • Simple to implement for WSI vendors • Solution is similar to blocked TIFF, which most WSI vendors use for storing WSI now • Simple to export from DICOM to TIFF • For compatibility with existing viewers, image analysis tools, and other WSI applications

16. Description of Proposed SolutionCharacteristics of Proposed Solution Issues not addressed by proposed solution • Compression type • Support uncompressed, lossless (e.g. LZW), and lossy (e.g. JPEG, JPEG2000) • As per current DICOM specification • Transport mechanism • Support image retrieval and JPIP • As per current DICOM specification • Multichannel / multispectral data • Solution addresses how to store images and pixels • Not composition / format of pixels • May need to extend DICOM specification to allow format and content of pixels to be defined for images in series